An odd little fungus that grows in cotton seeds and a little-known species of yeast are giving scientists an idea how organisms evolve and take on diverse functions. Two new studies report that the duplication of the genome of a primitive fungus more than 100 million years ago gave rise to common baker’s yeast.

The studies resolve an ongoing controversy over how the common yeast Saccharomyces cerevisiae evolved. The organism is widely studied because many of the genes that control the yeast’s function are also important in humans.

The new findings also give scientists clues about how gene duplications can drive evolution. While a backup copy of an essential gene continues to perform needed duties, a second copy is free to mutate and take on a new role in the organism.

“There have been two camps with different views of how yeast evolved,” says Manolis Kellis of the Broad Institute in Cambridge, Massachusetts, who participated in one of the new studies. “Some people believe a whole genome was duplicated and others believe smaller gene clusters were duplicated. We now have the missing piece of evidence that points to whole-genome duplication.”

Manolis and his colleagues sequenced a species of yeast called Kluyveromyces waltii. At the same time, a team led by Peter Philippsen of the University of Basel in Switzerland, sequenced the genome of the filamentous fungus Ashbya gossypii. Both studies suggest that a genome duplication in a common descendant led to the creation of baker’s yeast.

Ashbya has 4,718 genes on seven chromosomes and Kluyveromyces has 5,230 genes on eight chromosomes. Duplication of the genome of their common descendant created an organism with about 10,000 genes. Over time, most of the duplicated genes were lost, but some mutated and took on new functions. In the end, the baker’s yeast genome emerged with 5,714 genes on 16 chromosomes.

Philippsen, who studies the fungus Ashbya, notes that baker’s yeast and Ashbya have many genes in common but very different functions. Ashbya is a cotton pathogen, while baker’s yeast is used to make bread.

Baker’s yeast grows as a single-cell organism that grows and buds off into separate cells, whereas the fungus grows as a long filament containing many nuclei. The fungus grows from one end of a filament until it runs out of nutrients, creating a branched multi-cellular organism.

“These organisms have similar sets of genes, but very different lifestyles,” says Philippsen. “The big challenge now is to figure out why.”

One clue comes from looking at some of the duplicated genes. Although most of the duplicated genes have disappeared in baker’s yeast, many gene pairs remain, but have mutated to acquire different functions.

For example, one gene in baker’s yeast that is important for gene replication has a twin that silences, or shuts down, other genes. The researchers believe that many of these paired genes with different functions have driven evolution.

“When you have duplicated genes, many of these genes will be lost over time, because you only need one to do the job,” says Kellis. “But for some gene pairs, one gene has preserved the ancestral function while the other is free to evolve, sometimes taking on entirely new roles. This leads to innovation and the creation of new species.”

Baker’s yeast provides the first clear example that whole-genome duplication plays a role in evolution. Some researchers have proposed similar events in the evolution of plants and vertebrates.

“We would have to find an ancestor with a non-duplicated genome to see if similar events played a role in human evolution,” says Kellis. “So far, this hasn’t happened, but people are looking.”

Dietrich, F.S. et al. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Published online in Science March 4, 2004.